I use a HR monitor/watch as well. The technique I use is to find an exercise that approximates the calories per minute I burn and use it. I put in the time exercised and see if the total calories match my watch. I adjust 1 or 2 minutes either way to get the calories burned based on my watch.

For me, its more accounting for the exercise than what the specific exercise really was. For example, I find when I do the elliptical, I need to use the "running stairs" exercise to approximate the calories I burn rather than the "stair/tread" setting in Fitday.